Recovery plans for endangered invertebrates will improve with a better understanding of population dynamics and structure. Some spatially distributed structures beyond the classic metapopulation, including highly integrated patchy populations and core-satellite, maybe better suited for the recovery of endangered populations. In this study we examined the population dynamics of the Karner blue butterfly, Lycaeides melissa samuelis (Nabokov) [Lepidoptera: Lycaenidae], which is federally endangered in the USA, at eleven sites at Fort McCoy, Wisconsin. Adult L. m. samuelis butterflies were surveyed approximately weekly at each site using a straight line transect method. We used autocorrelation and partial autocorrelation function to look for patterns in the population dynamic, and tested for density-dependent growth and weather factors as potential explanatory factors of the yearly variation. We found non-declining or stable Karner blue populations at all eleven sites at Fort McCoy, a long-term trend and an alternating generational cycle. The trend occurred at seven of the eleven sites and was synchronous, suggesting that Karner blue butterflies were not functioning as a classic metapopulation and maybe functioning as a patchy metapopulation. We also found density-dependent growth and a positive relationship between early summer precipitation and population growth from the spring to summer generation. We suggest that aiming to recover patchy metapopulations will reduce monitoring costs, simplify reserve design, and create more robust populations, which are more likely to persist into the future.